Although I won’t make any claims about what the future of space travel will look like (I’ll leave that to @BoredElonMusk) there will absolutely be loyalty programs in the future in substantially the form that we have now.
The fundamentals of any system that encourages repeat business are precisely the core tenets of frequent flyer programs: recognize and reward (elite programs and rebates).
Credit cards will be less important for rewards in the future, because new technology will reduce the margins for processing payments (so banks won’t pay to incentivize transactions). But we’ll definitely be using miles for space travel!